QIMR Berghofer

Using whole-genome sequencing data to derive the homologous recombination deficiency scores.

Abstract

deficiency) in breast cancer samples. The score has utility in understanding tumour biology and may be indicative of response to certain therapeutic strategies. Studies have used whole-exome sequencing to derive the HRD score, however, with increasing use of whole-genome sequencing (WGS) to characterise tumour genomes, there has yet to be a comprehensive comparison between HRD scores derived by array versus WGS. Here we demonstrate that there is both a high correlation and a good agreement between array- and WGS-derived HRD scores and between the scores derived from WGS and downsampled WGS to represent shallow WGS. For samples with an HRD score close to threshold for stratifying HR proficiency or deficiency there was however some disagreement in the HR status between array and WGS data, highlighting the importance of not relying on a single method of ascertaining the homologous recombination status of a tumour.

Authors de Luca, Xavier M; Newell, Felicity; Kazakoff, Stephen H; Hartel, Gunter; McCart Reed, Amy E; Holmes, Oliver; Xu, Qinying; Wood, Scott; Leonard, Conrad; Pearson, John V; Lakhani, Sunil R; Waddell, Nicola; Nones, Katia; Simpson, Peter T
Journal NPJ BREAST CANCER
Pages 33
Volume 6
Date 1/08/2020
Grant ID
Funding Body National Health and Medical Research Council (NHMRC, Australia)
URL http://www.ncbi.nlm.nih.gov/pubmed/?term=10.1038/s41523-020-0172-0